5  R Packages for a Reproducibile Workflow

6 here package

• uses file path relative to the current project

# install here package
install.packages("here")

# read in a csv file
readr::read_csv(here::here("folder", "subfolder", "subsubfolder", "file.csv"))
# or
readr::read_csv(here::here("folder/subfolder/subsubfolder/file.csv"))

7 pacman package

• p_load() function checks if listed packages are already installed
  • if yes, loads them (as with library())
  • if no, installs and then lodas them (as long as they’re CRAN packages!)

# install pacman
install.packages("pacman")

# install and/or load packages
pacman::p_load(here,
               renv,
               kableExtra)

8 renv package

The renv packages stores your project-local environment. That is, it creates a time capsule of the R and package versions that you use within an R Project.

The benefits:

• your output is not dependent on whichever project version you currently have stored on your machine
  • e.g., if you come back to an analysis after a long time, the output should still be the same even if a certain package version has deprecated a function your analysis uses.
• makes the project reproducible for collaborators as well, who will likely have some different package versions (or will have missing packages) on their machine

The hard-to-get-your-head-around (imo):

• with each new R Project with a renv.lock file, you need to install all the necessary packages again (even if they’re on your machine)
  • this is because each renv doesn’t look beyond your project folder!
• remembering to update the renv.lock file frequently!

Running renv functions

Remember to always run renv functions in the console! You do not want e.g., renv initialising a new renv.lock file every time you render your documents.

8.1 Activate or init

• to initialise a new project-local environment:

renv::init()

8.2 Snapshot

• update renv.lock file

renv::snapshot()

After updating the renv.lock file, remember to commit/push these changes to git (if you’re using it)!

Version control

After updating the renv.lock file (i.e., running renv::snapshot()), remember to commit/push these changes to git (if you’re using git)! Otherwise, your renv.lock file will be outdated compared to your output.

8.3 Restore

• will restore your project to the most recent renv.lock file versions
  • this step follows snapshot(), which updates the renv.lock file
• very useful after updating R!

renv::restore()

8.4 Upgrade

• to update the renv package:

# upgrade renv version
renv::upgrade()

8.5 Update and Hydrate

# updates all packages (stored in renv.lock) in the renv cache
renv::hydrate(update = "all")

# update should have no effect now, but doesn't hurt to check
renv::update()

# now take a snapshot with the updated packages
renv::snapshot()

Version control (repeated)

After updating the renv.lock file (i.e., running renv::snapshot()), remember to commit/push these changes to git (if you’re using git)! Otherwise, your renv.lock file will be outdated compared to your output.